David Leemans

Seasonality of the soil biota of grazed and ungrazed hill grasslands

Temporal and spatial measurements of soil microbial biomass, activity and community structure and nematode abundance were made in grazed and ungrazed Agrostis-Festuca and Nardus dominated hill grasslands, with brown earth and podzolic soils, respectively. Microbial biomass and activity were significantly higher in podzolic soils with Nardus dominated vegetation, than in brown earth soils with Agrostis-Festuca vegetation. Phospholipid fatty acid analysis (PLFA) revealed differences in microbial community structure between soils. The ratio of fungal-to-bacterial fatty acids was higher in the brown earth than in the podzolic soil, whereas the diversity (Shannon-Weaver index) of PLFAs was greater in the podzolic soil. A large proportion of the microbial biomass (50%) and activity (40–70%) was within the surface 0–5 cm soil, with reduced amounts at lower depths of 5–10 cm and 10–15 cm. Microbial biomass and activity and nematode abundance showed pronounced summer maxima and winter minima. The long-term removal of sheep grazing from both grassland types resulted in significant reductions in microbial biomass and activity in the surface soil. The abundance of active soil fungi, measured as the fungal fatty acid 18:2ω6, was significantly reduced by the removal of sheep grazing, as was the ratio of fungal-to-bacterial fatty acids. Bacterial fatty acids were unaffected by the removal of sheep grazing. Possible mechanisms for these changes are discussed. Numbers of soil nematodes were significantly lower in the ungrazed sites. The effects of removing sheep grazing on nematodes and microbial community structure were most pronounced in brown earth soils. Factors responsible for these changes are discussed.

The short-term effects of cessation of fertiliser applications, liming, and grazing on microbial biomass and activity in a reseeded upland grassland soil

A field study was conducted to determine the influence of a short-term (2 year) cessation of fertiliser applications, liming, and sheep-grazing on microbial biomass and activity in a reseeded upland grassland soil. The cessation of fertiliser applications (N and NPK) on a limed and grazed grassland had no effect on microbial biomass measurements, enzyme activities, or respiration. Withholding fertiliser and lime from a grazed grassland resulted in significant reductions in both microbial biomass C (P<0.05) and dehydrogenase activity (P<0.05) by approximately 18 and 21%, respectively. The removal of fertiliser applications, liming, and grazing resulted in even greater reductions in microbial biomass C (44%, P<0.001) and dehydrogenase activity (31%, P<0.001), and significant reductions in microbial biomass N (P<0.005), urease activity (P<0.05), phosphatase activity (P<0.001), and basal respiration (P<0.05). The abundance of culturable bacteria and fungi and the soil ATP content were unaffected by changes in grassland managements. With the cessation of liming soil pH fell from 5.4 to 4.7, and the removal of grazing resulted in a further reduction to pH 4.5. A significant negative linear relationship (r2=0.97; P<0.01) was found between increasing soil acidity and dehydrogenase activity. Possible mechanisms influencing these changes are discussed.

Evidence in support of a role for plant-mediated proteolysis in the rumens of grazing animals

The present work aimed to differentiate between proteolytic activities of plants and micro-organisms during the incubation of grass in cattle rumens. Freshly cut ryegrass was placed in bags of varying permeability and incubated for 16 h in the rumens of dairy cows that had previously grazed a ryegrass sward, supplemented with 4 kg dairy concentrate daily. Woven polyester bags (50 microm pore size) permitted direct access of the micro-organisms and rumen fluid enzymes to the plant material. The polythene was impermeable even to small molecules such as NH(3). Dialysis tubing excluded micro-organisms and rumen enzymes/metabolites larger than 10 kDa. DM loss was 46.3 % in polyester, 36.2 % in polythene and 38.1 % in dialysis treatments. It is possible that the DM loss within polythene bags occurred due to a solubilisation of plant constituents (e.g. water-soluble carbohydrates) rather than microbial attachment/degradation processes. The final protein content of the herbage residues was not significantly different between treatments. Regardless of bag permeability, over 97 % of the initial protein content was lost during incubations in situ. Electrophoretic separation showed that Rubisco was extensively degraded in herbage residues whereas the membrane-associated, light-harvesting protein remained relatively undegraded. Protease activity was detected in herbage residues and bathing liquids after all incubation in situ treatments. Although rumen fluid contains proteases (possibly of plant and microbial origin), our results suggest that, owing to cell compartmentation, their activity against the proteins of intact plant cells is limited, supporting the view that plant proteases are involved in the degradation of proteins in freshly ingested herbage.

Modelling real-time simultaneous saccharification and fermentation of lignocellulosic biomass and organic acid accumulation using dielectric spectroscopy.

Dielectric spectroscopy (DS) is routinely used in yeast and mammalian fermentations to quantitatively monitor viable biomass through the inherent capacitance of live cells; however, the use of DS to monitor the enzymatic break down of lignocellulosic biomass has not been reported. The aim of the current study was to examine the application of DS in monitoring the enzymatic saccharification of high sugar perennial ryegrass (HS-PRG) fibre and to relate the data to changes in chemical composition. DS was capable of both monitoring the on-line decrease in PRG fibre capacitance (C=580 kHz) during enzymatic hydrolysis, together with the subsequent increase in conductivity (G=580 kHz) resulting from the production of organic acids during microbial growth. Analysis of the fibre fractions revealed >50% of HS-PRG lignocellulose had undergone enzymatic hydrolysis. These data demonstrated the utility of DS biomass probes for on-line monitoring of simultaneous saccharification and fermentation (SSF).

Microbial biomass and activity in a grassland soil amended with different application rates of silage effluent—A laboratory study

This laboratory study examines the impact of different application rates of silage effluent on the biomass and activity of microorganisms in a typical grassland soil (Denbigh series). Application rates ranged fi-om an equivalent of 0-5 l m(2) silage effluent, and amended soils were incubated at 25 degrees C for 32 days and periodically sampled (days 2, 4, 8, 16 and 32) for microbial biomass C, CO2 evolution and activities of various soil enzymes. After 2 and 4 days of incubation there was a significant trend of increasing microbial biomass C (P<0.001 and P<0.01, respectively), microbial respiration (CO2 evolution) (P<0.001), and dehydrogenase activity (P<0.01) with increasing rates of silage effluent application. Thereafter microbial biomass C, microbial respiration and dehydrogenase activity declined and were not significantly different from the unamended control soil. Specific respiration (respired C:biomass C) increased with increasing silage effluent application suggesting that microorganisms in amended soils may be physiologically stressed or that there is an increase in the proportion of effluent-derived bacteria relative to fungi in the amended soil. In a second experiment, there was a significant (r(2)=0.98; P<0.001) positive linear relationship between increasing rates of silage effluent application up to 30 l m(2) and microbial respiration. Dehydrogenase activity increased up to an equivalent application of 15 l m(2) and then declined, perhaps because high concentrations of certain chemical compounds with silage effluent have an adverse abiotic impact on the enzyme assay itself. The application of different rates of silage effluent had no effect on soil pH.

Characterization of the Microbiome along the Gastrointestinal Tract of Growing Turkeys

The turkey microbiome is largely understudied, despite its relationship with bird health and growth, and the prevalence of human pathogens such as Campylobacter spp. In this study we investigated the microbiome within the small intestine (SI), caeca (C), large intestine (LI), and cloaca (CL) of turkeys at 6, 10, and 16 weeks of age. Eight turkeys were dissected within each age category and the contents of the SI, C, LI, and CL were harvested. 16S rDNA based QPCR was performed on all samples and samples for the four locations within three birds/age group were sequenced using ion torrent-based sequencing of the 16S rDNA. Sequencing data showed on a genus level, an abundance of Lactobacillus, Streptococcus, and Clostridium XI (38.2, 28.1, and 13.0% respectively) irrespective of location and age. The caeca exhibited the greatest microbiome diversity throughout the development of the turkey. PICRUSt data predicted an array of bacterial function, with most differences being apparent in the caeca of the turkeys as they matured. QPCR revealed that the caeca within 10 week old birds, contained the most Campylobacter spp. Understanding the microbial ecology of the turkey gastrointestinal tract is essential in terms of understanding production efficiency and in order to develop novel strategies for targeting Campylobacter spp.

The Potential of Blue Lupins as a Protein Source, in the Diets of Laying Hens

Layers diets typically contain 15–20% soya due to its high crude protein content (ca. 36%). Reliance on soya for protein can result in large increases in cost of feed due to the law of supply and demand as a global commodity. Lupin grains have high protein content (35–40%) but previous experience with white lupins has shown toxic effects in poultry due to high levels alkaloids and poor performance due to anti-nutritional Non-starch polysaccharides (NSP). Here blue lupins either processed or whole were trialled for their potential as a protein source. Point of lay chickens (64) at 16 weeks of age were weighed and allocated to 16 coops of four hens. Coops, as the experimental unit, were randomly allocated to four treatments: layers mash with soya (Control); or layers mash with 150 g of lupin/kg diet with the lupin either: whole (Whole); dehulled (Dehulled) or dehulled + a solid state fermentation enzyme extract (SSF; 150 g/tonne DM). All diets were ground and formulated to be balanced for energy, crude protein and essential amino acids using NIRS. No difference in growth rate, final hen weight, DM and water intake, eggs per day, mean egg weight, yellowness of yolk or chroma was found between treatments. There was a trend (P<0.1) for the SSF treatment to produce less heavy shells and a significant effect for the lupin treatments to have redder yolks (P<0.001). Fecal DM and bacterial counts were not different and there was no sign of enteritis or intestinal tissue hyperplasia from hen autopsies. Inclusion of blue lupins in the diet of laying hens at a rate of 150 g/kg DM resulted in no adverse effects in production or hen health and could be used as part of a balanced ration with inclusion of NSP degrading enzymes to reduce reliance on soya protein.